This track shows the coverage of Nanopore sequences from
Kim et al. 2020
obtained after in-vitro reverse transcription and tiling PCR of SARS-CoV-2
genomes. This is not direct RNA sequencing, but multiplex PCR on DNA, followed by
sequencing. The coverage shown here does not allow to draw conclusions on RNA
modifications or RNA editing, but indicates regions of the genome that are
harder to sequence with Nanopore sequencing.
Display Conventions and Configuration
Sequence coverage of every bp is shown. All reads were used.
- ARTIC primers: a set of well-known primers used for PCR + Nanopore sequencing.
- Kim Transcripts: transcripts as determined with direct RNA sequencing by Kim et al.
- Kim RNA Brkpts: locations where RNA tends to break, as determined by direct
sequencing by Kim et al. 2020
- Kim RNA Modif: modified bases in the direct RNA sequencing relative to the IVT
Minimap2 alignments BAM files were processed with bamCoverage.
Kim D, Lee JY, Yang JS, Kim JW, Kim VN, Chang H.
The Architecture of SARS-CoV-2 Transcriptome.
Cell. 2020 May 14;181(4):914-921.e10.
PMID: 32330414; PMC: PMC7179501